The axon initial segment of cortical neurons contains the so-called cisternal organelle, an enigmatic formation of stacked endoplasmic reticulum and interdigitating plates of electron-dense material. This organelle shows many structural similarities to the spine apparatus, a cellular organelle found in a subpopulation of dendritic spines. Whereas roles in calcium signaling and protein trafficking have been proposed for the spine apparatus, little is yet known about the physiological function of its putative axonal counterpart. Considering the structural similarity of these two organelles, we hypothesized that synaptopodin, a protein essential for the formation of the dendritic spine apparatus, could also be a component of the cisternal organelle. By using immunofluorescence microscopy, we found that synaptopodin is indeed located within the axon initial segments of principal neurons in the mouse neocortex and hippocampus. Pre-embedding immunogold labeling demonstrated a close association of synaptopodin immunoreactivity with the dense plates of cisternal organelles. In synaptopodin-deficient mice, ultrastructural analysis of identified axon initial segments of CA1 pyramidal cells revealed a lack of cisternal organelles similar to the reported lack of spine apparatuses in these mutants. However, in vitro patch clamp recording of mutant neurons showed that the lack of cisternal organelles did not lead to any changes in basic electrophysiological parameters of action potentials. Taken together, our data demonstrate that synaptopodin is an essential component of the cisternal organelle of axons and of the dendritic spine apparatus, two organelles that are structurally and molecularly related.